Jekyll2026-04-10T19:28:45+00:00https://chrisphdoan.com/feed.xmlHomeBioinformaticsStarsolo2025-10-26T00:00:00+00:002025-10-26T00:00:00+00:00https://chrisphdoan.com/2025/10/26/STARsoloSTARsolo is faster than CellRanger
https://www.biorxiv.org/content/10.1101/2021.05.05.442755v1.full

]]>Longevity Companies2025-10-26T00:00:00+00:002025-10-26T00:00:00+00:00https://chrisphdoan.com/2025/10/26/longevity-companiesLeading anti-aging companies/startups
  1. Calico
  2. Altos Lab
  3. Retro Biosciences
  4. Shift Biocience
]]>Shift Bioscience2025-10-25T00:00:00+00:002025-10-25T00:00:00+00:00https://chrisphdoan.com/2025/10/25/Shift-BioscienceSB000 a single gene https://www.biorxiv.org/content/10.1101/2025.06.05.657370v1

]]>Clustering Cells in Single Cell Analysis2025-09-18T00:00:00+00:002025-09-18T00:00:00+00:00https://chrisphdoan.com/bioinformatics/2025/09/18/cluster-cellsHow do we cluster cells in single-cell RNA-seq?

Graph-based clustering (Seurat) is the most popular method.
FindNeighbors() has default k = 20, k-nearest neighbor (kNN), 20 cells
https://bioconductor.org/books/3.15/OSCA.basic/clustering.html

  1. Similarity is computed. Euclidean distance or cosine similarity
  2. Nearest neighbors are found
  3. A graph (network) is built. Cells = nodes, neighbor relationships = edges, stronger similarity = stronger edge weight.
  4. Communities (clusters) are detected. Clustering algorithms in single cell: Louvain or Leiden
]]>Welcome to My Blog2025-09-18T00:00:00+00:002025-09-18T00:00:00+00:00https://chrisphdoan.com/bioinformatics/biomedical/2025/09/18/welcome-to-my-blogI’ll be sharing insights about bioinformatics, data analysis, and my research journey here. Stay tuned for posts about:

  • Single-cell RNA sequencing analysis
  • Cell-cell communication in Alzheimer’s disease
  • Best practices for reproducible research
  • Tips for bioinformatics workflows

Coming Soon

I’m working on detailed tutorials and case studies from my research. Check back soon!

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